Hi! I’m trying to have multiple marker files because I would like them to have different radius and coloring distance. I figured out that I can create new marker files by “marker #5 1,1,1 radius 100”, for example. However, if I add new markers, the new marker always goes to the first marker file, instead of the selected marker file that I want. Any help is really appreciated! Best, Shiqing
Hi Shiqing, In your example command, #5 is telling it to add to marker model #5. If there is a different marker set it would have a different model number. So if you are adding the marker with a command, you can control it directly by the model number in that command. However, the example command you gave isn't quite right, maybe you meant: marker #5 position 1,1,1 radius 100 "marker" command details: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/marker.html> You are probably talking about adding the marker with the mouse, however. In that case, you are right: I don't see a way to control which marker model is used. Maybe we did not plan for people to have multiple marker models. So maybe this is a type of control that can be added in the future. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/markerplacement.html> Sorry about that, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 29, 2021, at 7:29 PM, SHIQING LIAO via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi!
I’m trying to have multiple marker files because I would like them to have different radius and coloring distance. I figured out that I can create new marker files by “marker #5 1,1,1 radius 100”, for example. However, if I add new markers, the new marker always goes to the first marker file, instead of the selected marker file that I want. Any help is really appreciated!
Best, Shiqing
Hi Shiqing, I added a menu to the Marker Placement panel to choose which marker set is used when adding markers with the mouse. Also the "New" button will make a new marker set. These improvements will be in tonight's ChimeraX builds. Tom
On Jun 30, 2021, at 8:47 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Shiqing, In your example command, #5 is telling it to add to marker model #5. If there is a different marker set it would have a different model number. So if you are adding the marker with a command, you can control it directly by the model number in that command. However, the example command you gave isn't quite right, maybe you meant:
marker #5 position 1,1,1 radius 100
"marker" command details: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/marker.html>
You are probably talking about adding the marker with the mouse, however. In that case, you are right: I don't see a way to control which marker model is used. Maybe we did not plan for people to have multiple marker models. So maybe this is a type of control that can be added in the future.
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/markerplacement.html>
Sorry about that, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 29, 2021, at 7:29 PM, SHIQING LIAO via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi!
I’m trying to have multiple marker files because I would like them to have different radius and coloring distance. I figured out that I can create new marker files by “marker #5 1,1,1 radius 100”, for example. However, if I add new markers, the new marker always goes to the first marker file, instead of the selected marker file that I want. Any help is really appreciated!
Best, Shiqing
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Hi Elaine and Tom, Thank you so much! I am amazed by the speed of response and update! Best, Shiqing On Wed, Jun 30, 2021 at 11:42 AM Tom Goddard <goddard@sonic.net> wrote:
Hi Shiqing,
I added a menu to the Marker Placement panel to choose which marker set is used when adding markers with the mouse. Also the "New" button will make a new marker set. These improvements will be in tonight's ChimeraX builds.
Tom
On Jun 30, 2021, at 8:47 AM, Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Shiqing, In your example command, #5 is telling it to add to marker model #5. If there is a different marker set it would have a different model number. So if you are adding the marker with a command, you can control it directly by the model number in that command. However, the example command you gave isn't quite right, maybe you meant:
marker #5 position 1,1,1 radius 100
"marker" command details: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/marker.html>
You are probably talking about adding the marker with the mouse, however. In that case, you are right: I don't see a way to control which marker model is used. Maybe we did not plan for people to have multiple marker models. So maybe this is a type of control that can be added in the future.
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/markerplacement.html>
Sorry about that, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 29, 2021, at 7:29 PM, SHIQING LIAO via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi!
I’m trying to have multiple marker files because I would like them to have different radius and coloring distance. I figured out that I can create new marker files by “marker #5 1,1,1 radius 100”, for example. However, if I add new markers, the new marker always goes to the first marker file, instead of the selected marker file that I want. Any help is really appreciated!
Best, Shiqing
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Elaine and Tom, I actually have a related question on marker files. I tried to color my density by “color zone #2 near #4 distance 70”, for example. However, it seems that I can only have one marker file colored (they are mutually exclusive). For example, if I want to color area around another model by “color zone #2 near #5”, the coloring done by the previous command near #4 will disappear. Best, Shiqing On Wed, Jun 30, 2021 at 12:04 PM SHIQING LIAO <shiqing03@g.ucla.edu> wrote:
Hi Elaine and Tom,
Thank you so much! I am amazed by the speed of response and update!
Best, Shiqing
On Wed, Jun 30, 2021 at 11:42 AM Tom Goddard <goddard@sonic.net> wrote:
Hi Shiqing,
I added a menu to the Marker Placement panel to choose which marker set is used when adding markers with the mouse. Also the "New" button will make a new marker set. These improvements will be in tonight's ChimeraX builds.
Tom
On Jun 30, 2021, at 8:47 AM, Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Shiqing, In your example command, #5 is telling it to add to marker model #5. If there is a different marker set it would have a different model number. So if you are adding the marker with a command, you can control it directly by the model number in that command. However, the example command you gave isn't quite right, maybe you meant:
marker #5 position 1,1,1 radius 100
"marker" command details: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/marker.html>
You are probably talking about adding the marker with the mouse, however. In that case, you are right: I don't see a way to control which marker model is used. Maybe we did not plan for people to have multiple marker models. So maybe this is a type of control that can be added in the future.
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/markerplacement.html>
Sorry about that, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 29, 2021, at 7:29 PM, SHIQING LIAO via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi!
I’m trying to have multiple marker files because I would like them to have different radius and coloring distance. I figured out that I can create new marker files by “marker #5 1,1,1 radius 100”, for example. However, if I add new markers, the new marker always goes to the first marker file, instead of the selected marker file that I want. Any help is really appreciated!
Best, Shiqing
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Shiqing, You would need to do it in one command, e.g. color zone #2 near #4,5 <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone> I hope this helps, Elaine
On Jun 30, 2021, at 12:09 PM, SHIQING LIAO via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine and Tom,
I actually have a related question on marker files. I tried to color my density by “color zone #2 near #4 distance 70”, for example. However, it seems that I can only have one marker file colored (they are mutually exclusive). For example, if I want to color area around another model by “color zone #2 near #5”, the coloring done by the previous command near #4 will disappear.
Best, Shiqing
Hi Elaine, Thank you! For this situation, however, if I do it in one command, I am not able to set different distance for each marker file. Is there a way of doing that? Best, Shiqing On Wed, Jun 30, 2021 at 12:45 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Shiqing, You would need to do it in one command, e.g.
color zone #2 near #4,5
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone>
I hope this helps, Elaine
On Jun 30, 2021, at 12:09 PM, SHIQING LIAO via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine and Tom,
I actually have a related question on marker files. I tried to color my density by “color zone #2 near #4 distance 70”, for example. However, it seems that I can only have one marker file colored (they are mutually exclusive). For example, if I want to color area around another model by “color zone #2 near #5”, the coloring done by the previous command near #4 will disappear.
Best, Shiqing
No, sorry. Maybe it would be possible by writing python, but I wouldn't know how to do it. Elaine
On Jun 30, 2021, at 12:47 PM, SHIQING LIAO <shiqing03@g.ucla.edu> wrote:
Hi Elaine,
Thank you! For this situation, however, if I do it in one command, I am not able to set different distance for each marker file. Is there a way of doing that?
Best, Shiqing
On Wed, Jun 30, 2021 at 12:45 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Shiqing, You would need to do it in one command, e.g.
color zone #2 near #4,5
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone>
I hope this helps, Elaine
On Jun 30, 2021, at 12:09 PM, SHIQING LIAO via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine and Tom,
I actually have a related question on marker files. I tried to color my density by “color zone #2 near #4 distance 70”, for example. However, it seems that I can only have one marker file colored (they are mutually exclusive). For example, if I want to color area around another model by “color zone #2 near #5”, the coloring done by the previous command near #4 will disappear.
Best, Shiqing
Hi Shiqing, I improved the "color zone" command so you can use the option "farColor keep" and do successive color zone colorings while keeping the older colorings that are outside the distance range. For example, color zone #1 near #2 distance 50 color zone #1 near #3 distance 100 farColor keep One limitation is that if you then change the surface shape, for example change the volume threshold on a contour surface, then it only preserves the most recent color zone command coloring. Another limitation is that if you use the "sharpEdges true" option then the old coloring is lost. Tom
On Jun 30, 2021, at 12:49 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
No, sorry. Maybe it would be possible by writing python, but I wouldn't know how to do it. Elaine
On Jun 30, 2021, at 12:47 PM, SHIQING LIAO <shiqing03@g.ucla.edu> wrote:
Hi Elaine,
Thank you! For this situation, however, if I do it in one command, I am not able to set different distance for each marker file. Is there a way of doing that?
Best, Shiqing
On Wed, Jun 30, 2021 at 12:45 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Shiqing, You would need to do it in one command, e.g.
color zone #2 near #4,5
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone>
I hope this helps, Elaine
On Jun 30, 2021, at 12:09 PM, SHIQING LIAO via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine and Tom,
I actually have a related question on marker files. I tried to color my density by “color zone #2 near #4 distance 70”, for example. However, it seems that I can only have one marker file colored (they are mutually exclusive). For example, if I want to color area around another model by “color zone #2 near #5”, the coloring done by the previous command near #4 will disappear.
Best, Shiqing
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Hi Tom, Thank you so much! Really appreciate it! Best, Shiqing On Wed, Jun 30, 2021 at 2:31 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Shiqing,
I improved the "color zone" command so you can use the option "farColor keep" and do successive color zone colorings while keeping the older colorings that are outside the distance range. For example,
color zone #1 near #2 distance 50 color zone #1 near #3 distance 100 farColor keep
One limitation is that if you then change the surface shape, for example change the volume threshold on a contour surface, then it only preserves the most recent color zone command coloring. Another limitation is that if you use the "sharpEdges true" option then the old coloring is lost.
Tom
On Jun 30, 2021, at 12:49 PM, Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
No, sorry. Maybe it would be possible by writing python, but I wouldn't know how to do it. Elaine
On Jun 30, 2021, at 12:47 PM, SHIQING LIAO <shiqing03@g.ucla.edu> wrote:
Hi Elaine,
Thank you! For this situation, however, if I do it in one command, I am not able to set different distance for each marker file. Is there a way of doing that?
Best, Shiqing
On Wed, Jun 30, 2021 at 12:45 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Shiqing, You would need to do it in one command, e.g.
color zone #2 near #4,5
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone>
I hope this helps, Elaine
On Jun 30, 2021, at 12:09 PM, SHIQING LIAO via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine and Tom,
I actually have a related question on marker files. I tried to color my density by “color zone #2 near #4 distance 70”, for example. However, it seems that I can only have one marker file colored (they are mutually exclusive). For example, if I want to color area around another model by “color zone #2 near #5”, the coloring done by the previous command near #4 will disappear.
Best, Shiqing
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participants (3)
-
Elaine Meng -
SHIQING LIAO -
Tom Goddard